AMBER Archive (2008)

Subject: RE: AMBER: AMBER force field for glycolipid

From: Matthew Tessier (matthew.tessier_at_gmail.com)
Date: Thu Oct 09 2008 - 08:57:59 CDT

Dr. Abel,
The GLYCAM06 force field includes lipid parameters that are designed to work
with the existing GLYCAM06 and GLYCAM04 force fields. I can't speak to
using the ff force field for the tails, but GLYCAM06 and GLYCAM04 have been
designed to work with FF99/FF99SB for proteins. The main concern with using
the GLYCAM and FF force fields is the 1-4 scaling factor. The FF force
field uses a 1-4 scaling factor while GLYCAM does not. I've included the
reference for the GLYCAM06 Lipids force field below. Also, you may want to
consider using the latest version of GLYCAM06 which is available at
http://www.glycam.com/gl_params.html . These files should be placed in
their AMBER directories for use.

Tessier, M.B., DeMarco, M.L., Yongye, A.B., Woods, R.J. Extension of the
GLYCAM06 biomolecular force field to lipids, lipid bilayers and glycolipids.
Molecular Simulation, 34(4) 2008, pages 349-363.

Matthew Tessier
mbt3911_at_uga.edu
matthew.tessier_at_gmail.com
Woods' Lab Room 1092
Complex Carbohydrate Research Center - University of Georgia

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Stephane Abel
Sent: Wednesday, October 08, 2008 8:25 AM
To: amber_at_scripps.edu
Subject: AMBER: AMBER force field for glycolipid

Dear AMBERS users

For my work, I would like to simulate maltose-glycolipids micelles in
water. So by searching in the literature I found this paper

1. Chong, T.T., R. Hashim, and R.A. Bryce, Molecular Dynamics
Simulation of Monoalkyl Glycoside Micelles in Aqueous Solution:
Influence of Carbohydrate Headgroup Stereochemistry. J. Phys. Chem. B,
2006. 110(10): p. 4978-4984.
 

In this article, the authors used the force field from the cornell et
al. ff for the alkane tail et glycam_2000 for the surfactant headgroup.
So I would like to compare the micelles structures obtained with AMBER
ff with those previously performed with CHARMM ff. So my questions are:

- Is this combination of ff is well suited for this work ?

- If not, does it exist more recent (i.e. up to date) potential ?

Thank you very for your advices

Dr Stephane Abel

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